Hi Ming,
can you include your mdin file and also the cpptraj script? then people
will be able to see what you're doing.
On Tue, Mar 23, 2021 at 12:31 AM Ming Tang <m21.tang.qut.edu.au> wrote:
> Hey Carlos,
>
> Thanks for your suggestion. The system shows the restraint is working as
> two compounds initially closer than r2 angstroms were pulled away from each
> other until they are more than r2 angstroms away due to the repulsive
> force. But after the simulation goes on for a while, some compounds do not
> repel each other even if there are close to each other. I extracted the
> distance between two restrained groups from the output file generated by
> DUMPAVE and calculated the distance via cpptraj distance command.
> Initially, their values are same because the two molecules are in the same
> box, but after a while (the length of the time depends on the selected
> groups and the simulation), their values are different, e.g., the distance
> calculated from distance command is smaller than r2, whereas the distance
> from DUMPAVE is much larger than r2. Therefore, the two close groups are
> not restrained. I have been outputting and calculating the distance per 1
> step, and after restart the simulation multiple times, I came across the
> above same issue. I am totally not sure what is wrong here.
>
> Thanks,
> Ming
>
>
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Friday, 19 March 2021 1:05 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Apply Lennar-Jones potential between small molecules
>
> I would not think about what happens after autoimage- that's not what is
> going on in your simulation and the restraints will only be applied to what
> happens during MD.
> focus on the input structure that you give to sander or pmemd, and whether
> you use imaging during MD or not. also on how you set up the pairs and
> distances for the restraints.
> can you simplify the problem to a single restraint that you think isn't
> working, and explain what your restraint is, the initial coordinates for
> that pair, and why you think it isn't working during MD?
>
>
>
> On Thu, Mar 18, 2021 at 10:53 AM Ming Tang <m21.tang.qut.edu.au> wrote:
>
> > Yes. I tried both iwrap=0 and 1, and the distance is same and not real
> > (not equal to the distance after the cpptraj autoimage process)
> > ________________________________
> > From: Carlos Simmerling <carlos.simmerling.gmail.com>
> > Sent: Thursday, 18 March 2021 8:35 PM
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] Apply Lennar-Jones potential between small molecules
> >
> > what do you mean by "before autoimage"? autoimage is a cpptraj command,
> but
> > it sounds like you are talking about what happens in the MD run.
> > do you have iwrap=1 in your simulation?
> >
> >
> > On Thu, Mar 18, 2021 at 12:15 AM Ming Tang <m21.tang.qut.edu.au> wrote:
> >
> > > Dear Carlos and David,
> > >
> > > Thank you very much for your guidance. Yes, I found that a positive rk2
> > > does the right thing and the problem lies in how the system calculates
> > the
> > > distance between two IGRs. I found out that the system calculates the
> > > distance based on the coordinate before autoimage, and therefore the
> > small
> > > molecules do not get close in the trajectory before the autoimage
> > process.
> > > I guess this comes from the periodic boundary condition setting.
> > >
> > > Is there a way to fix this?
> > >
> > > Many thanks,
> > > Ming
> > > ________________________________
> > > From: Carlos Simmerling <carlos.simmerling.gmail.com>
> > > Sent: Tuesday, 16 March 2021 11:41 PM
> > > To: AMBER Mailing List <amber.ambermd.org>
> > > Subject: Re: [AMBER] Apply Lennar-Jones potential between small
> molecules
> > >
> > > On Tue, Mar 16, 2021 at 8:56 AM David A Case <david.case.rutgers.edu>
> > > wrote:
> > >
> > > > On Tue, Mar 16, 2021, Carlos Simmerling wrote:
> > > >
> > > > >yes negative rk gives an inverted parabola, so it is repulsive if it
> > is
> > > > >outside the flat region.
> > > >
> > > > I'm a little confused here, and would recommend careful testing if
> you
> > > are
> > > > setting rk2 to a negative number. I've not done that but it *sounds*
> > > > dangerous. Probably a good idea to numerically plot the function vs.
> > > > distance, and make sure you are getting the behavior you want.
> > > >
> > > >
> > > Dave is right, this can be really dangerous since it goes to infinitely
> > > negative energies. I've used it and technically it does work, but it's
> > > probably much safer to use other options. I should have been more
> careful
> > > in giving caution along with my reply!
> > >
> > > re-reading the original question, a negative rk2 will make them
> > ATTRACTIVE
> > > below r2, and it doesn't sound like this is what you want. *For
> repulsive
> > > interaction below r2 you want a positive rk2.*
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Received on Tue Mar 23 2021 - 04:00:02 PDT
